scPDB - 3d2d entry

Protein Data Bank Entry:

PDB ID : 3d2d

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2008-05-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Reticuline oxidase
ID:	RETO_ESCCA
AC:	P30986
Organism:	Eschscholzia californica
Reign:	Eukaryota
TaxID:	3467
EC Number:	1.21.3.3

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	45.304
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.120	783.000

% Hydrophobic	% Polar
56.90	43.10
According to VolSite

Ligand :

HET Code:	REN
Formula:	C19H24NO4
Molecular weight:	330.398 g/mol
DrugBank ID:	-
Buried Surface Area:	67.06 %
Polar Surface area:	63.36 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
28.0735	34.4643	21.421

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C10	CE1	TYR- 106	4.3	0	Hydrophobic	false
C16	CZ2	TRP- 165	4.15	0	Hydrophobic	false
C25	CZ2	TRP- 165	3.38	0	Hydrophobic	false
C23	SD	MET- 182	4.47	0	Hydrophobic	false
C23	CB	SER- 280	3.97	0	Hydrophobic	false
C24	CD2	LEU- 282	3.4	0	Hydrophobic	false
C23	CD1	LEU- 295	3.64	0	Hydrophobic	false
C5	CB	ASP- 352	4.45	0	Hydrophobic	false
C7	CB	ASP- 352	3.81	0	Hydrophobic	false
O4	OD2	ASP- 352	3.12	169.29	H-Bond (Ligand Donor)	false
O4	OD1	ASP- 352	2.87	120.46	H-Bond (Ligand Donor)	false
C7	CB	ARG- 354	4.24	0	Hydrophobic	false
C10	CE1	PHE- 356	3.95	0	Hydrophobic	false
C7	CD2	PHE- 356	3.47	0	Hydrophobic	false
C10	CG2	THR- 358	4.46	0	Hydrophobic	false
C16	CE1	PHE- 386	4.05	0	Hydrophobic	false
C18	CB	ALA- 388	3.41	0	Hydrophobic	false
O22	ND2	ASN- 390	3.11	158.94	H-Bond (Protein Donor)	false
O20	OE1	GLU- 417	2.78	154.16	H-Bond (Ligand Donor)	false
C16	CD1	ILE- 419	4.37	0	Hydrophobic	false
C10	CG2	ILE- 419	4.01	0	Hydrophobic	false
C7	CB	ALA- 421	3.53	0	Hydrophobic	false